They don't really do it that often or need to, but do you mean specifically against the MC or a group that was created maybe for other purposes but then ended up against the MC ?
Happens a lot in Daoist Gu/ Gu Daoist Master after a few hundred chapters MC is a complete loner. Most groups he forms is with people who want to kill him
They could also be like a bunch of people of different values but got together to fight a common enemy and ended up being friends.
Rokujouma no Shinryakusha!? has the protagonist form a group from various factions, and the individual antagonists of each faction end up forming their own group in response. Toaru Majutsu no Index has several groups with cross-faction membership, especially in New Testament.
Ah well, there's very often some group of another 'heavenly lords' 'Top 10s' and whatnots, usually with some name trying to sound awesome who very often start a fight with the MC one way or another.
Nope. Just people who want to kill him. He also has no qualms about killing them. Purely temporary allies. Also pure evil.
World of Cultivation kind of fits - especially after the MC leaves his sect - though it takes a while to get to that point. In Star Rank Hunter they also form a group with people from all over the galaxy beloging to different powers - beware that this is more of a sub-plot that often gets ignored (mostly focused solely on the mc)